MicroRNAs (
miRNAs) are key regulators in various physiological and
pathological processes via post-transcriptional regulation of gene expression. The honey bee (Apis mellifera) is a key model for highly social species, and its complex social behaviour can be interpreted theoretically as changes in gene regulation, in which
miRNAs are thought to be involved. We used the SOLiD sequencing system to identify the repertoire of
miRNAs in the honey bee by sequencing a mixed small
RNA library from different developmental stages. We obtained a total of 36,796,459 raw sequences; of which 5,491,100 short sequences were fragments of
mRNA and other noncoding RNAs (ncRNA), and 1,759,346 reads mapped to the known
miRNAs. We predicted 267 novel honey bee
miRNAs representing 380,182 short reads, including eight
miRNAs of other insects in 14,107,583 genome-mapped sequences. We verified 50 of them using stem-loop reverse-transcription PCR (RT-PCR), in which 35 yielded PCR products. Cross-species analyses showed 81 novel
miRNAs with homologues in other insects, suggesting that they were authentic
miRNAs and have similar functions. The results of this study provide a basis for studies of the
miRNA-modulating networks in development and some intriguing phenomena such as caste differentiation in A. mellifera.